advantage of package over native installation?

Can anybody point out what the main advantages are of installing various applications (phpMyAdmin, RoundCube etc.) from ISPConfig packages as opposed to doing regular, native installations using the os's default installation tools (like aptitude on Debian). Thusfar the only advantage I can see is the entry in the "Tools" menu. The most obvious disadvantage I see is that ISPConfig packages are usually somewhat behind.

1) The phpadmin and roundcube packages from your linux distribution will not work in the locations where they were installed.You will have to tweak the configuration manually.
2) Some of the ISPconfig pacakges are patched to read data from the ISPconfig database.